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Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same(More)
BACKGROUND Chromohalobacter salexigens (formerly Halomonas elongata DSM 3043) is a halophilic extremophile with a very broad salinity range and is used as a model organism to elucidate prokaryotic osmoadaptation due to its strong euryhaline phenotype. RESULTS C. salexigens DSM 3043's metabolism was reconstructed based on genomic, biochemical and(More)
Deciphering the complex network structure is crucial in drug target identification. This study presents a framework incorporating graph theoretic and network decomposition methods to analyze system-level properties of the comprehensive map of the epidermal growth factor receptor (EGFR) signaling, which is a good candidate model system to study the general(More)
The challenging task of studying and modeling complex dynamics of biological systems in order to describe various human diseases has gathered great interest in recent years. Major biological processes are mediated through protein interactions, hence there is a need to understand the chaotic network that forms these processes in pursuance of understanding(More)
The identification of protein-protein interactions (PPIs) and their networks is vitally important to systemically define and understand the roles of proteins in biological systems. In spite of development of numerous experimental systems to detect PPIs and diverse research on assessment of the quality of the obtained data, a consensus--highly reliable,(More)
Saccharomyces cerevisiae has been widely used for bio-ethanol production and development of rational genetic engineering strategies leading both to the improvement of productivity and ethanol tolerance is very important for cost-effective bio-ethanol production. Studies on the identification of the genes that are up- or down-regulated in the presence of(More)
Halomonas smyrnensis AAD6T is a gram negative, aerobic, and moderately halophilic bacterium, and is known to produce high levels of levan with many potential uses in foods, feeds, cosmetics, pharmaceutical and chemical industries due to its outstanding properties. Here, the whole-genome analysis was performed to gain more insight about the biological(More)
Brevibacillus thermoruber strain 423 is a Gram-positive, spore-forming, aerobic, and thermophilic bacterium that produces mannogalactoglucan exopolysaccharide (EPS). We report the draft genome sequence of B. thermoruber 423, which will accelerate research on the cellular organization of thermophilic bacteria, as well as the rational design and optimization(More)
Brevibacillus thermoruber 423 is a Gram-positive, motile, red-pigmented, spore-forming, aerobic, and thermophilic bacterium that is known to produce high levels of exopolysaccharide (EPS) with many potential uses in food, feed, cosmetics, and pharmaceutical and chemical industries. This bacterium not only is among the limited number of reported thermophilic(More)
Marine biotechnology can be considered as the use of marine bioresources as the target or source of biotechnological applications. Despite many successes have been achieved in marine biotechnology, still many gaps remain to be filled in our basic knowledge on marine science before it could be fully exploited. Systems biology focuses on complex interactions(More)